Basic question for mask making for local refinement

Local Refinement
10

I have a few questions concerning this topic. I am trying the local refinement job. So far I have done the following:

  1. NU refinement
  2. created volume around region of interest in ChimeraX
  3. Imported volume in cryosparc and turned it into a mask A
  4. Took the same mask A to make an inverted mask B that contains everything but the region of interest.
  5. Ran particle subtract job with B. I find it confusing that the particles look the same as before to me. However a 2D classification job as suggested elsewhere on this forum seems to confirm that it worked. Why do the particles not look different after the subtraction?
  6. Ran local refinement.

In principle this seems to work, but I am not sure whether step 4) is correct or if mask B should only contain the part of the protein that I do not want to refine.

Thanks for your help!